The one thing that I hate or I am annoyed about this game. I was in this one area and I took out every enemy in the area. But when I took out the last guy with a brick, it seemed to spawn 3 more baddies to pop up in the area. Where the heck did they come from? The area that I am referring to is the area where you just enter a quarantine zone after arriving in Pittsburg. You just escaped the surprise attack. There is three guys out side and there is a building that has two floors. After carefully taking down every enemy. I know even from smashing the guy with a brick that no one else would be in the area to hear it. **bleep** is this crap? Each one of them popped out behind a table that I just walked by before. Why do developers do this kinda of thing. People don't just pop into existence in real life so I don't understand why they do it in this game?
Your obsession about body odor might be the answer. Joel just reeks of body odor that enemies smell it from a mile away. They just can't help but spawn everywhere and take out that smelly dude.
I believe those extra bad guys are backup that was called for most likely after one of them found a dead body? I noticed that they will react the same way after finding a dead body as they do if they see you kill someone. The sound of gun fire might do it as well cause I had 3-4 extra guys to deal with after entering David's town with Joel which were not there after I had to reload and sucessfully sneak killed my way through.